Kaiser Vera B, van Tuinen Marcel, Ellegren Hans
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden.
Mol Biol Evol. 2007 Jan;24(1):338-47. doi: 10.1093/molbev/msl164. Epub 2006 Oct 31.
Using standard phylogenetic methods, it can be hard to resolve the order in which speciation events took place when new lineages evolved in the distant past and within a short time frame. As an example, phylogenies of galliform birds (including well-known species such as chicken, turkey, and quail) usually show low bootstrap support values at short internal branches, reflecting the rapid diversification of these birds in the Eocene. However, given the key role of chicken and related poultry species in agricultural, evolutionary, general biological and disease studies, it is important to know their internal relationships. Recently, insertion patterns of transposable elements such as long and short interspersed nuclear element markers have proved powerful in revealing branching orders of difficult phylogenies. Here we decipher the order of speciation events in a group of 27 galliform species based on insertion events of chicken repeat 1 (CR1) transposable elements. Forty-four CR1 marker loci were identified from the draft sequence of the chicken genome, and from turkey BAC clone sequence, and the presence or absence of markers across species was investigated via electrophoretic size separation of amplification products and subsequent confirmation by DNA sequencing. Thirty markers proved possible to type with electrophoresis of which 20 were phylogenetically informative. The distribution of these repeat elements supported a single homoplasy-free cladogram, which confirmed that megapodes, cracids, New World quail, and guinea fowl form outgroups to Phasianidae and that quails, pheasants, and partridges are each polyphyletic groups. Importantly, we show that chicken is an outgroup to turkey and quail, an observation which does not have significant support from previous DNA sequence- and DNA-DNA hybridization-based trees and has important implications for evolutionary studies based on sequence or karyotype data from galliforms. We discuss the potential and limitations of using a genome-based retrotransposon approach in resolving problematic phylogenies among birds.
运用标准的系统发育方法，当新的谱系在遥远的过去且在短时间内演化时，很难确定物种形成事件发生的顺序。例如，鸡形目鸟类（包括鸡、火鸡和鹌鹑等知名物种）的系统发育树通常在较短的内部分支处显示出较低的自展支持值，这反映了这些鸟类在始新世的快速分化。然而，鉴于鸡及相关家禽物种在农业、进化、普通生物学和疾病研究中的关键作用，了解它们的内部关系非常重要。最近，诸如长散在核元件和短散在核元件标记等转座元件的插入模式已被证明在揭示复杂系统发育的分支顺序方面很强大。在这里，我们基于鸡重复序列1（CR1）转座元件的插入事件，解析了一组27种鸡形目物种的物种形成事件顺序。从鸡基因组草图序列和火鸡细菌人工染色体克隆序列中鉴定出44个CR1标记位点，并通过扩增产物的电泳大小分离以及随后的DNA测序确认来研究物种间标记的有无。30个标记经电泳证明可以分型，其中20个在系统发育上具有信息性。这些重复元件的分布支持了一个单一的无同塑分支图，该图证实冢雉、凤冠雉、新大陆鹌鹑和珠鸡形成雉科的外类群，并且鹌鹑、雉鸡和鹧鸪各自都是多系群。重要的是，我们表明鸡是火鸡和鹌鹑的外类群，这一观察结果在以前基于DNA序列和DNA - DNA杂交的树中没有得到显著支持，并且对基于鸡形目序列或核型数据的进化研究具有重要意义。我们讨论了使用基于基因组的逆转座子方法解决鸟类中有问题的系统发育的潜力和局限性。
